On igneous and metamorphic substrates populations of Coryphantha tuberculosa mostly have unbranched stems. D. Weniger (1984) considered such populations to represent C. varicolor Tiegel; their reproductive structures, however, are identical to those of C. tuberculosa. Without seeds or flowers, mature specimens from such populations sometimes are indistinguishable from C. dasyacantha [hence the synonym C. dasyacantha var. varicolor (Tiegel) L. D. Benson].

Coryphantha tuberculosa is the type species of the segregate genus Escobaria, which includes the coryphanthas with pitted seeds.